;
> Yujing
>
>
>
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>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sara Teso Cuesta
> *Sent:* Friday, June 30, 2023 1:05 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] dcmunpack
;
> Yujing
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sara Teso Cuesta
> *Sent:* Friday, June 30, 2023 1:05 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] dcmunpack
: 1 2 …’ in the output. I
believe should be one of these series Nos.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sara Teso Cuesta
Sent: Friday, June 30, 2023 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dcmunpack: Issues with the -run argument
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to use dcmunpack to transform dicom images to a nifti format
inside a FSFAST formatted directory (
https://secure-web.cisco.com/1JV-FemocV4fiLoKofgFHZ2hQTt_nlpR8LAqJEXvFr3d88Y9d8_5ARW5ZwWfjra1Get0gYobq4LmRSdujgu
Sent: Tuesday, May 2, 2023 12:17 PM
To: Greve, Douglas N.,Ph.D. ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dcmunpack behavior with scouts
External Email - Use Caution
It seems to be working fine: -keep-scouts does keep the scouts and removing it
discards the scouts.
There
External Email - Use Caution
It seems to be working fine: -keep-scouts does keep the scouts and removing it
discards the scouts.
There was some errors for some runs but they were the same for dcmunpack as
distributed in dev so I did not bother investigating further.
I had to re
, Freesurfer support list
Subject: Re: [Freesurfer] dcmunpack behavior with scouts
I've attached a new version of dcmunpack. Try running this with -keep-scouts
and without -keep-scouts
Let me know if this runs successfully in both situations (I'm using you as my
tester:)
On 4/18/2023 10:51
External Email - Use Caution
I've attached a new version of dcmunpack. Try running this with
-keep-scouts and without -keep-scouts
Let me know if this runs successfully in both situations (I'm using you
as my tester:)
On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote:
Sorry
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It only ignores them if you use -auto-runseq Is that what you are doing?
On 4/5/2023 11:00 AM, Proulx, Jean Sebastien wrote:
Dear Freesurfer Team,
The help of dcmunpack says it will ignore scout scans. Is there
perhaps a hidden flag to avoid that b
Dear Freesurfer Team,
The help of dcmunpack says it will ignore scout scans. Is there perhaps a
hidden flag to avoid that behavior? We are running multiple scouts throughout a
session to combat head motion. Getting those images along the rest would allow
visualizing that motion offline.
Thanks
just install FS
On 10/27/2022 4:56 PM, Jang, Woo Ju Albert W.,PhD wrote:
Hi, I need to unpack dcm files to my local workstation via /dcmunpack/
command. Is it possible to install this command on my local workstation?
Best,
Albert
___
Freesurfer
Hi, I need to unpack dcm files to my local workstation via dcmunpack command.
Is it possible to install this command on my local workstation?
Best,
Albert
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailma
Sam way as with unpacksdcmdir, ie, by specifying -run run subdir format
stemname
Another way it to use the -auto-runseq format , eg -auto-runseq mgz
this will output all the runs preprending the run number and protocol name
If you are using 7.3.X, then you can also add --dcm2niix which will
spe
Good afternoon,
Quick question about unpacking:
The instructions I have from a previous staff member said to do this:
In folder where files are going, type: unpacksdcmdir -src
-targ . -scanonly scanout.txt
So what I submit is:
unpacksdcmdir -src
/cluster/archive/338/siemens/Prisma_fit-67026-202
You can use eg, -auto-runseq mgz, this will unpack all scans as
runno.seqname.mgz (eg, 0004.mprage.mgz). You might want to add
-no-exit-on-error so that it does not exit when it finds a run that it
cannot convert.
On 1/14/2022 8:44 PM, Shi, Yuelin wrote:
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Hello FreeSurfer Developers,
I am using dcmunpack to unpack a data session that is composed of many
series/runs. It seems that I can only feed in unpacking rules for one of the
runs at a time by the "-run run subdir format stemname" command. Also for
running into trouble using this command!
Best,
Matt
From: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Thursday, November 19, 2020 at 7:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dcmunpack command not found
External Email - Use Caution
Hello, i have been trying to
External Email - Use Caution
Hello, i have been trying to use the dcmunpack command and it always says
command not found, i searched in the archives and some said it could be because
the tcsh or csh wasnt installed however i have both installed (which tcsh and
which csh return t
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Hi all,
I have installed freesurfer and when I type in “dcmunpack -src . -scanonly
scan.log”, I get “command not found.” Please advise. Thank you!
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Freesurfer@nmr.mgh.harvard.edu
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Dear Greve,
Thank you so much. It s finally fixed and now is working properly.
Regards
On Fri, 9 Nov 2018 at 02:50, Greve, Douglas N.,Ph.D.
wrote:
> It actually looks like it completed and created the desired output file.
> Did you check it? Tho
It actually looks like it completed and created the desired output file.
Did you check it? Those errors are generated because it is trying to
figure out whether the file is a diffusion scan. You can turn it off by
setting
setenv FS_LOAD_DWI 0
or for bash
export FS_LOAD_DWI=0
On 11/07/2018 09:5
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I tried this way, but I got lots of errors, as the attached file. What is
the problem? Is there anything wrong with my data? Because I am using the
online databases which I think it might be back to 2009 ish.
Thanks
On Thu, 8 Nov 2018 at 11:55, Greve,
You have to specify an output directory with -targ and the runs you want
to unpack with -run. See the help (ie, run dcmunpack with -help)
On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
> I was going to reconstruct MPRAGE imag
External Email - Use Caution
Hello Freesurfer Developers,
I was going to reconstruct MPRAGE images from GE 3T machine.
First I used this command:
*dcmunpack -src . -scanonly scan.log*
It made just *scan.log* file for me. Then I used this command:
*unpacksdcmdir -src / -targ
-scan
without more info it is impossible for me to tell
On 12/21/2017 03:21 PM, Keiko McCreary wrote:
> Hi Doug,
>
> Do you have any idea why it is taking so long? I just ran 1092 files
> at 8AM this morning and it is still going...
>
> Thank you!
>
>
> Keiko
>
> On Fri, Oct 13, 2017 at 9:03 AM, Dougl
Hi Doug,
Do you have any idea why it is taking so long? I just ran 1092 files at 8AM
this morning and it is still going...
Thank you!
Keiko
On Fri, Oct 13, 2017 at 9:03 AM, Douglas Greve
wrote:
> It should not take that long. For only that number of scans it should only
> take a few min.
>
>
It should not take that long. For only that number of scans it should
only take a few min.
On 10/12/17 1:10 PM, Keiko McCreary wrote:
Hi There,
Could someone tell me how long approximately dcmunpack should take? (I
have 243 files and it has been "interrogating" now for 2 hours.
Thank you!
Hi There,
Could someone tell me how long approximately dcmunpack should take? (I have
243 files and it has been "interrogating" now for 2 hours.
Thank you!
Keiko
--
J. Keiko McCreary, PhD
Postdoctoral Fellow
SARTAN-AD Clinical Research Coordinator (Lethbridge Site)
Canadian Centre for Behavio
Hi Steve, if the same volume is distributed over multiple directories,
then it will surely fail (actually, it is mri_convert that assumes that
all files for a given volume will be in the same directory). I don't
know of anyone else who has had this problem, even those who are
scanning for 20 mi
There is a bug in the new *dcmunpack* that replaces the earlier *
unpacksdcmdir* when it is unpacking a "fragmented" dicom directory, i.e.
one in which the files were saved to DVD incrementally during the scan, as
opposed to dicom files that are saved all at once, after all the scanning
is complete
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